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De-novo emergence of SINE retroposons during the early evolution of passerine birds

BACKGROUND: Passeriformes (“perching birds” or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is...

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Detalles Bibliográficos
Autores principales: Suh, Alexander, Bachg, Sandra, Donnellan, Stephen, Joseph, Leo, Brosius, Jürgen, Kriegs, Jan Ole, Schmitz, Jürgen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729268/
https://www.ncbi.nlm.nih.gov/pubmed/29255493
http://dx.doi.org/10.1186/s13100-017-0104-1
Descripción
Sumario:BACKGROUND: Passeriformes (“perching birds” or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes. RESULTS: Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri – songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching. CONCLUSIONS: We propose that the early evolution of passerines was unusual among birds in that it was accompanied by de-novo emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13100-017-0104-1) contains supplementary material, which is available to authorized users.